Job:PhD position in evolutionary genomics
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About the position

The Department of Animal and Aquacultural Sciences, Faculty of Biosciences at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year Ph.D.–position in evolutionary genomics. The position is financed by the RCN-funded project SalmoSV and linked to FHF-funded project SynchroSmolt. The projects seek to understand the genome evolution and phenotype-affecting variants following a recent whole-genome duplication of Atlantic salmon.

Genomic structural variants including deletions, duplications, inversions, and translocations of genetic sequences, are rich resources for genetic diversity. In particular, Atlantic salmon genomes show extreme levels of genomic structural variants, likely due to their unique history of recent whole-genome duplication. Structural variants in Atlantic salmon genomes are one of the most promising frontiers in both evolutionary genomics and aquacultural genomics. However, due to their complex nature, which and how structural variants have driven adaptive evolution with functional advantage are yet to be clarified. Long-read sequencing is a cutting-edge technique to identify previously undiscovered structural variants. In our ongoing project, the genomic map of Atlantic salmon with long-read sequences is getting ready for deep investigation.

The goal of this project is to reveal adaptive structural variants have driven and their functional advantages by integrating omics data sets. The Ph.D. project will focus on the estimation of the effects of structural variants on various phenotypes bioinformatically. The other focus of this Ph.D. project is to reveal the adaptive evolution of structural variants of farmed salmon under domestication compared to their wild counterparts. The candidate will work in close collaboration with other Ph.D. students, postdoctoral researchers, and senior researchers.

The successful candidate will join CIGENE (https://cigene.no/), a multidisciplinary genome biology research group. CIGENE has established excellent wet lab facilities (CIGENE genomics lab) for automated high-throughput omics analyses and gene-editing technology, as well as the connected CIGENE Bioinformatics & Computational Unit with IT specialists to support the transfer, storage and analysis of omics data, currently administering a computer cluster. The unit will make use of both our local computer cluster with 580 CPUs, 4TB RAM and 600TB storage and national computational resources (NOTUR/Sigma2 and NORSTORE).

References:

1 Lien, et al., https://doi.org/10.1038/nature17164 [2]Bertolotti, et al., https://doi.org/10.1038/s41467-020-18972-x [3] Stenlokk, et al., https://dx.doi.org/10.1098/rstb.2021.0195

Main tasks

The main goal of this project is to reveal the adaptive evolution and functional effect of structural variants in Atlantic salmon. The main tasks are bioinformatic analyses of publicly available genomics and transcriptomics dataset in the view of evolution.

Specifically:

Literature review to explore relevant studies and methods Estimate the effect of genomic structural variants on smoltification, the physiological “metamorphose” from fresh water to seawater in Atlantic salmon. Compare population-scale genomes of geographically broadly distributed wild Atlantic salmon and farmed Atlantic salmon and identify adaptive genomic evolution. Extend the evolutionary analysis at the cross-species scale and reveal the deeper evolutionary history of target genes. Publish three peer-reviewed papers under the supervision of advisors

The successful candidate is expected to enter a plan for the progress of the work towards a Ph.D. degree during the first months of the appointment, with a view to completing a doctorate within the Ph.D. scholarship period. Presentation of findings at international conferences or/and attending international workshops/visiting relevant researchers are highly encouraged and financially supported.

For more info and Apply, please visit:

https://www.jobbnorge.no/en/available-jobs/job/228438/phd-scholarship-on-evolutionary-genomics

evolution transcriptome genomics bioinformatics • 186 views
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